+Open data
-Basic information
Entry | Database: PDB / ID: 1ps3 | ||||||
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Title | Golgi alpha-mannosidase II in complex with kifunensine | ||||||
Components | Alpha-mannosidase IIMannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase | ||||||
Keywords | HYDROLASE / glycosyl hydrolase / mannosidase / N-TERMINAL ALPHA-BETA DOMAIN / THREE HELIX BUNDLE / 2 C-TERMINAL BETA BARRELS | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shah, N. / Kuntz, D.A. / Rose, D.R. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Comparison of Kifunensine and 1-Deoxymannojirimycin Binding to Class I and II alpha-Mannosidases Demonstrates Different Saccharide Distortions in Inverting and Retaining Catalytic Mechanisms Authors: Shah, N. / Kuntz, D.A. / Rose, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ps3.cif.gz | 240 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ps3.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 1ps3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1ps3 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1ps3 | HTTPS FTP |
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-Related structure data
Related structure data | 1htyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 119593.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / Cell line: S2 cells References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 986 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-KIF / |
#5: Chemical | ChemComp-MRD / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, MPD, Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9504 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2002 |
Radiation | Monochromator: Horizontally bent Si(111), assymetrically cut with water cooled Cu block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9504 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 153548 / Num. obs: 144642 / % possible obs: 85.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 5.25 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.1 / % possible all: 83.3 |
Reflection | *PLUS % possible obs: 94.2 % / Num. measured all: 759620 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 83.3 % / Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HTY Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refinement | *PLUS Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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